Steps

• [x] PR job which runs a build, rustfmt, and clippy
• [x] Master build job with status badge in README.md
• [x] New release job, which builds a Changelog from commit history and opens a draft release
• [x] New release job attaches pre-built binaries for Linux
• [x] New release job attaches pre-built binaries for MacOS (x86_64)

I'm a big believer that every open source project destined for success must make contributions (and maintenance) easy. A solid CI is a cornerstone of that.

If you can spare a week or two, I'd offer to do this for you.

Currently it operates on the current index of entries, not the original index. This causes mis-sorting if the input sequences were already permuted before the order is calculated.

The next step of #2.

The next time you want to release a new version, simply push a git tag of the new version. It must be of format vN.N.N (And it does have to be all three point versions, unlike your first release tag.)

That will trigger this workflow. It does these steps:

1. Generates a changelog from the previous tag, based on git history
2. Creates a new GitHub release draft (for you to manually review and publish), with the changelog in the the description
3. Builds MacOS X (Intel) and Linux (x86_64) builds, ZIPs them up with license and readme
4. Attaches the ZIP files to the release as assets

If you see the draft release but no builds attached, and the master branch was indeed passing, just wait 5 minutes and try again. Due to action dependencies, the job creates the draft release first, then starts on the binary builds.

You can see an example workflow run here.

The next part of #2.

This also adds a couple badges to the README. In my experience, these help people understand the state of the project, and may (tacitly) encourage contributions.

The first step on #2.

The CI will not run until the files are committed to master. Here is a run to show you what it will look like.

I also ran rustfmt, because the CI now requires code to pass both it and clippy. If you don't like the changes it made, let me know. Some parameters can be tweaked.

Hi, i wanted to say thank you for making this alignment viewer, i really like it!

I have had some problems viewing MSAs of RNAs with modified residues. The problem seems to be that with all the modified RNA residues that exist, the sequences contain a lot of unusual characters.

A database of modified RNA residues can be found here: https://iimcb.genesilico.pl/modomics/modifications

There seem to be two problems as far as i can see

• unicode characters, e.g. °

>tdbR00000266|Bos_taurus|9913|Leu|°AA
-GUCAGLAUGLCMGAGU--GGDCPAAGGCLCCAGACU°AAKPPCUGGJ-CPCC---GUAU----GGAGG-?GUGGGTPCG"AUCCCACUUCUGACACCA

Error message:

ERROR when loading FASTA: Not all input sequences are the same length. Expected sequence length 99, seq "tdbR00000266|Bos_taurus|9913|Leu|°AA" has length 100.

• autodetection trying to interpret sequences as amino-acids

>tdbR00000270|Avian_myeloblastosis_virus|11866|Met|BAU
-GCCUCCUUALCGCAGDA-GGN--AGCGCRPCAGPCUBAU6APCUGAAG-------------------7D??UGAGTPCG"ACCUCAGAGGGGGCACCA

Error message:

ERROR when loading FASTA: Sequence "tdbR00000270|Avian_myeloblastosis_virus|11866|Met|BAU" cannot be understood as amino acids.

My suggestion would be to have additional command-line options to

• allow unicode
• force dna, rna, aa mode without autodetect

Not sure how to deal with it in visualisation. I guess one color for any nonstandard RNA base would be ok.

What do you think? I could try and make the changes if you agree

Data source:

Data was downloaded from tRNAdb:

http://trna.bioinf.uni-leipzig.de/DataOutput/Search

On the Search Database page, choose tRNA sequences and then press the search database button. This will return RNA sequences with modified sequences. You can save them by selecting the select all sequences of search checkbox on the search results page, and then saving the sequences by choosing Download alignment in the drop down button next to the checkbox.

It would be nice to work with stdin, but unfortunately, crossterm does not seem to support it at the moment.

As soon as crossterm fixes the issue or provide a workaround, implement reading from stdin.